[gmx-users] Cannot write trajectory frame; maybe you are out of disk space

[Mark Abraham]

If you can rule out file permissions issues (because you wrote files
earlier), and actually running out of disk, usually that would suggest a
flaky network file system.

Mark


On Mon, Apr 21, 2014 at 4:09 PM, Andrew Bostick
<andrew.bostick1 at gmail.com>wrote:

> Dear gromacs users
>
> I am doing md simulation on the a protein with 190 residues.
>
> I did minimization and equilibration without problem and error.
>
> But in production run step (last md simulation with 15000000 steps),
> in step 6500000, I encountered with following error:
>
> File input/output error:
> Cannot write trajectory frame; maybe you are out of disk space.
>
> my mdp file is as follows:
>
> -----------------------------------------------------------------------------------------
> title        = opls Protein MD
> ; Run parameters
> integrator    = md                    ; leap-frog integrator
> nsteps        = 15000000                ; 0.002 * 500000 = 1000 ps, 30 ns
> dt             = 0.002                    ; 2 fs
> ; Output control
> nstxout        = 3000                     ; save coordinates every 2 ps
> nstvout        = 3000                     ; save velocities every 2 ps
> nstxtcout    = 3000                     ; xtc compressed trajectory output
> every 2 ps
> nstenergy    = 3000                     ; save energies every 2 ps
> nstlog        = 3000                     ; update log file every 2 ps
> energygrps  = Protein Ion
> ; Bond parameters
> continuation    = yes                ; Restarting after NPT
> constraint_algorithm = lincs        ; holonomic constraints
> constraints    = all-bonds                ; all bonds (even heavy atom-H
> bonds) constrained
> lincs_iter    = 1                        ; accuracy of LINCS
> lincs_order    = 4                        ; also related to accuracy
> ; Neighborsearching
> ns_type        = grid                    ; search neighboring grid cells
> nstlist        = 5                        ; 10 fs
> rlist        = 1.0                     ; short-range neighborlist cutoff
> (in nm)
> rcoulomb    = 1.0                     ; short-range electrostatic cutoff
> (in nm)
> rvdw        = 1.0                     ; short-range van der Waals cutoff
> (in nm)
> ; Electrostatics
> coulombtype    = PME                    ; Particle Mesh Ewald for
> long-range electrostatics
> pme_order    = 4                        ; cubic interpolation
> fourierspacing    = 0.16                ; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl        = V-rescale                ; modified Berendsen thermostat
> tc-grps        = Protein Non-Protein    ; two coupling groups - more
> accurate
> tau_t        = 0.1    0.1                ; time constant, in ps
> ref_t        = 300     300                ; reference temperature, one for
> each group, in K
> ; Pressure coupling is on
> pcoupl        = Parrinello-Rahman        ; Pressure coupling on in NPT
> pcoupltype    = isotropic                ; uniform scaling of box vectors
> tau_p        = 2.0                    ; time constant, in ps
> ref_p        = 1.0                    ; reference pressure, in bar
> compressibility = 4.5e-5            ; isothermal compressibility of water,
> bar^-1
> ; Periodic boundary conditions
> pbc        = xyz                        ; 3-D PBC
> ; Dispersion correction
> DispCorr    = EnerPres                ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel        = no                    ; Velocity generation is off
>
> -----------------------------------------------------------------------------------------
>
> If I use df -h command to know disk space, I obtained following
> information:
>
> Filesystem      Size  Used Avail Use% Mounted on
> /dev/sda3       220G   14G  196G   7% /
> none            4.0K     0  4.0K   0% /sys/fs/cgroup
> udev            3.0G  4.0K  3.0G   1% /dev
> tmpfs           607M  1.3M  606M   1% /run
> none            5.0M     0  5.0M   0% /run/lock
> none            3.0G  152K  3.0G   1% /run/shm
> none            100M   64K  100M   1% /run/user
> /dev/sda6       245G   61G  184G  25% /media/pdfco/my dear
> /dev/sda2       220G   85G  136G  39% /media/pdfco/Windows
> /dev/sda5       245G   43G  202G  18% /media/pdfco/nazif
>
> ------------------------------------------------------------------------------------------
>
> Is my computer system suitable for this md simulation?
>
> How to solve this error?
>
> Any help will highly appreciated.
> --
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